Table 2.
Crystallographic data collection and refinement statistics
| Crystal data | wild type·guanine (2PWU) | Glu235Gln pH 5.5 (2OKO) | Glu235Gln pH 8.5 (2Z1V) | Glu235Gln·guanine (2POT) |
|---|---|---|---|---|
| A. Data processing | ||||
| Space group | C2 | C2 | C2 | C2 |
| a, b, c (Å) | 90.2, 64.5, 70.8 | 90.4, 65.2, 70.5 | 90.8, 65.2, 70.5 | 89.1, 63.7, 71.1 |
| β (deg.) | 92.8 | 96.4 | 96.1 | 92.9 |
| Resolution rangea (Å) | 50-1.77 (1.80 -1.77) | 50-1.50 (1.53-1.50) | 20–1.55 (1.58–1.55) | 50-1.80 (1.83-1.80) |
| Total no. of reflections | 105,401 | 210,241 | 132,929 | 90,611 |
| No. of unique reflections | 36,424 | 59,104 | 56,093 | 33,979 |
| Completenessa (%) | 94.8 (83.9) | 91.5 (85.1) | 95.6 (78.5) | 97.6 (83.4) |
| Redundancy | 2.8 | 3.5 | 2.3 | 2.5 |
| R(I)syma,b (%) | 4.4 (38.9) | 3.2 (15.9) | 5.8 (23.9) | 4.1 (46.7) |
| I/σ (I) a | 22 (2.3) | 33 (8.0) | 16 (3.8) | 21 (1.5) |
| B. Refinement | ||||
| Rworkc/Rfreed (%) | 20.0/27.1 | 12.5/17.4 | 14.3/20.3 | 21.9/28.6 |
| No. of atoms/residues (molecules) | ||||
| Protein | 2,702/358 | 2,824/365 | 2,860/369 | 2,688/355 |
| Water | 101 | 346 | 305 | 86 |
| Glycerol (cryo buffer) | 18/3 | 96/16 | 24/4 | 42/7 |
| Ligand | 14/1 | --- | --- | 11/1 |
| Mean B-factors (Å2) | ||||
| Protein | 32.8 | 21.8 | 21.6 | 39.0 |
| Water | 34.0 | 34.8 | 31.3 | 40.4 |
| Glycerol (cryo buffer) | 52.6 | 48.1 | 39.4 | 62.6 |
| Ligand | 60.4 | --- | --- | 53.5 |
| rmsd angle (°) | 2.0 | 2.2 | 2.2 | 2.0 |
| rmsd bond (Å) | 0.007 | 0.011 | 0.010 | 0.006 |
| (An)isotropic refinement | isotropic | anisotropic | anisotropic | isotropic |
| Crystal data | Glu235Gln·BIH (2Z1W) | Glu235Gln·preQ0 (2PWV) | Glu235Gln·preQ1 (2Z1X) | |
|
| ||||
| A. Data processing | ||||
| Space group | C2 | C2 | C2 | |
| a, b, c (Å) | 90.9, 65.3, 70.6 | 90.5, 65.2, 70.4 | 89.0, 64.2, 70.6 | |
| β (deg.) | 96.7 | 96.3 | 93.1 | |
| Resolution rangea (Å) | 50-1.63 (1.66-1.63) | 20–1.70 (1.73–1.70) | 50-1.63 (1.66-1.63) | |
| Total no. of reflections | 170,346 | 124,483 | 103,473 | |
| No. of unique reflections | 47,068 | 42,679 | 42,180 | |
| Completenessa (%) | 92.5 (83.9) | 98.3 (96.9) | 89.8 (93.1) | |
| Redundancy | 3.6 | 2.8 | 2.3 | |
| R(I)syma,b (%) | 3.2 (17.2) | 5.9 (49.1) | 7.8 (31.6) | |
| I/σ(I) a | 33 (8.3) | 12 (2.2) | 24 (2.0) | |
| B. Refinement | ||||
| Rworkc/Rfreed (%) | 13.2/19.4 | 20.1/24.5 | 15.3/21.6 | |
| No. of atoms/residues (molecules) | ||||
| Protein | 2,801/362 | 2,799/361 | 2,790/364 | |
| Water | 298 | 228 | 172 | |
| Glycerol (cryo buffer) | 60/10 | 36/6 | 48/8 | |
| Ligand | 15/1 | 13/1 | 13/1 | |
| Mean B-factors (Å2) | ||||
| Protein | 23.5 | 22.8 | 25.7 | |
| Water | 34.0 | 28.6 | 32.9 | |
| Glycerol (cryo buffer) | 54.8 | 48.5 | 53.0 | |
| Ligand | 22.2 | 24.9 | 25.2 | |
| rmsd angle (°) | 2.1 | 2.1 | 2.1 | |
| rmsd bond (Å) | 0.010 | 0.009 | 0.008 | |
| (An)isotropic refinement | anisotropic | isotropic | anisotropic | |
a
number in parentheses is for highest resolution shell
b
R(I)sym = Σ |I −〈I〉|/ΣI with I representing the observed intensities and 〈I〉 representing the mean observed intensity
c
Rwork = Σhkl |Fo − Fc|/Σhkl |Fo|.
d
Rfree was calculated as for Rwork but on 5 % of the data excluded from the refinement